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Biomedical subjects

Y Singer

Publications and source records attributed to Y Singer.

14 recordsLinked to original sources
PubMed2001

Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences.

Accurately estimating probabilities from observations is important for probabilistic-based approaches to problems in computational biology. In this paper we present a biologically-motivated method for estimating probability distributions over discrete alphabets from observations using a mixture model of common ancestors. The method is an extension of substitution matrix-based probability estimation methods. In contrast to previous such methods, our method has a simple Bayesian interpretation and has the advantage over Dirichlet mixtures that it is both effective and simple to compute for large alphabets. The method is applied to estimate amino acid probabilities based on observed counts in an alignment and is shown to perform comparably to previous methods. The method is also applied to estimate probability distributions over protein families and improves protein classification accuracy.

Amino Acid Sequence↗
PubMed2000

Expression, purification and applications of staphylococcal protein A fused to cellulose-binding domain.

Because staphylococcal Protein A (ProtA) binds specifically to IgG, it has been used for many immunological manipulations, most notably antibody purification and diagnostics. Immobilization is required for most of these applications. Here we describe a genetic-engineering approach to immobilizing ProtA on cellulose, by fusing it to cellulose-binding domain (CBD) derived from the cellulose-binding Protein A of Clostridium cellulovorans. The bifunctional fusion protein was expressed in Escherichia coli, recovered on a cellulose column and purified by elution at alkaline pH. ProtA-CBD was used to purify IgG from rabbit serum and its ability to bind IgG from different sources was determined. The bifunctional chimaeric protein can bind up to 23.4 mg/ml human IgG at a ratio of 1 mol of ProtA-CBD/2 mol of human IgG, and can purify up to 11.6 mg/ml rabbit IgG from a serum. The ability to bind functionally active CBD-affinity reagents to cellulosic microtitre plates was demonstrated. Our results indicate that a combination of CBD-affinity reagents and cellulosic microtitre plates is an attractive diagnostics matrix for the following reasons: (i) cellulose exhibits very low non-specific binding; and (ii) CBD-fusion proteins bind directly to cellulose at high density. A unique signal-amplification method was developed based on the ability of ProtA-CBD to link stained cellulose particles to primary antibody in a Western blot.

Animals↗
PubMed2000

Protein family classification using sparse Markov transducers.

In this paper we present a method for classifying proteins into families using sparse Markov transducers (SMTs). Sparse Markov transducers, similar to probabilistic suffix trees, estimate a probability distribution conditioned on an input sequence. SMTs generalize probabilistic suffix trees by allowing for wild-cards in the conditioning sequences. Because substitutions of amino acids are common in protein families, incorporating wildcards into the model significantly improves classification performance. We present two models for building protein family classifiers using SMTs. We also present efficient data structures to improve the memory usage of the models. We evaluate SMTs by building protein family classifiers using the Pfam database and compare our results to previously published results.

Algorithms↗
PubMed1999

[Second degree atrioventricular block in Graves' disease].

Cardiac tachyarrhythmias are common in thyrotoxicosis. We report an uncommon case of a 53-year-old woman with Grave's disease who developed second degree A-V block while euthyroid on propylthiouracil. The most likely mechanism is an autoimmune response causing infiltration of the cardiac conduction pathways.

Antithyroid Agents↗
PubMed1998

Where do family practice patients go in case of emergency?

OBJECTIVE: To determine the annual incidence of patient-defined emergencies and patients' use of emergency services at a family medicine teaching unit. DESIGN: Cross-sectional survey. SETTING: Hospital-based family medicine teaching unit in Montreal. PARTICIPANTS: Registered patients attending a family medicine teaching unit during 11 consecutive weekdays. MAIN OUTCOME MEASURES: Annual incidence of patient-defined medical emergencies and use of emergency services at the unit. RESULTS: Eligible patients made 815 visits during the study period; 584 usable questionnaires were returned for a response rate of 71.7%. In the previous 12 months, 37% of patients reported at least one medical emergency. For their last emergency, 42% reported using at least one of the emergency services offered by the clinic. Only 19% of patients with after-hours emergencies reported using our on-call system. Although socioeconomic and clinical variables did not predict the incidence of patient-defined emergencies, multivariate analysis revealed three significant predictors for use: patients with the practice for 5 or more years were more likely to use our services, while patients 75 and older and those with emergencies after hours were less likely to use our services. CONCLUSIONS: In an urban group family practice, annual incidence of medical emergencies among registered patients was 37%. Those whose most recent emergency occurred after hours used the clinics' emergency on-call services disappointingly little.

Adolescent↗
PubMed1997

Switching portfolios.

A constant rebalanced portfolio is an asset allocation algorithm which keeps the same distribution of wealth among a set of assets along a period of time. Recently, there has been work on on-line portfolio selection algorithms which are competitive with the best constant rebalanced portfolio determined in hindsight (Cover, 1991; Helmbold et al., 1996; Cover and Ordentlich, 1996). By their nature, these algorithms employ the assumption that high returns can be achieved using a fixed asset allocation strategy. However, stock markets are far from being stationary and in many cases the wealth achieved by a constant rebalanced portfolio is much smaller than the wealth achieved by an ad hoc investment strategy that adapts to changes in the market. In this paper we present an efficient portfolio selection algorithm that is able to track a changing market. We also describe a simple extension of the algorithm for the case of a general transaction cost, including the transactions cost models recently investigated in (Blum and Kalai, 1997). We provide a simple analysis of the competitiveness of the algorithm and check its performance on real stock data from the New York Stock Exchange accumulated during a 22-year period. On this data, our algorithm outperforms all the algorithms referenced above, with and without transaction costs.

Algorithms↗
PubMed1995

Clinical characteristics of delayed and immediate-onset combat-induced post-traumatic stress disorder.

The aim of the current study is to examine the clinical characteristics of war-related disturbances among veterans with delayed and immediate-onset post-traumatic stress disorder (PTSD). One hundred twenty-five veterans who sought help for war-related disturbances, 8 years after the 1982 Lebanon War, filled out the PTSD Inventory, Impact of Event Scale, and SCL-90. Their scores were compared with those of 370 treated combat stress reaction casualties who filled out the questionnaires a year after the same war. Findings indicate that veterans from the delayed-helpseeking group suffer from a higher rate (92 vs. 59%) and a greater intensity of PTSD, more intrusive tendencies, and more severe general psychiatric symptomatology than those of the immediate-helpseeking group. These findings indicate that a fair number of combatants still seek help for war-related disturbances almost a decade after the war. The complex relationship between delayed-helpseeking and delayed-onset PTSD is discussed.

Adult↗
PubMed1994

Dynamical encoding of cursive handwriting.

A model-based approach to on-line cursive handwriting analysis and recognition is presented and evaluated. In this model, on-line handwriting is considered as a modulation of a simple cycloidal pen motion, described by two coupled oscillations with a constant linear drift along the line of the writing. By slow modulations of the amplitudes and phase lags of the two oscillators, a general pen trajectory can be efficiently encoded. These parameters are then quantized into a small number of values without altering the writing intelligibility. A general procedure for the estimation and quantization of these cycloidal motion parameters for arbitrary handwriting is presented. The result is a discrete motor control representation of the continuous pen motion, via the quantized levels of the model parameters. This motor control representation enables successful word spotting and matching of cursive scripts. Our experiments clearly indicate the potential of this dynamic representation for complete cursive handwriting recognition.

Computer Simulation↗
PubMed1992

Post-traumatic stress disorder in Israel during the Gulf War.

During the Gulf War, the Unit for the Treatment of Combat Reactions within the Central Military Mental Health Center of the IDF was active in treating soldiers suffering from post-traumatic stress disorder (PTSD). Of the 72 referrals, all but 2 were cases of a reactivation of a previous stress reaction. The implications for residual vulnerability amongst even apparently remitted cases are discussed in this essay.

Adolescent↗
PubMed1985

Determination of specific cytomegalovirus IgM antibodies using infected air dried cells and isolated nuclei by immunoperoxidase assay.

A simple immunoperoxidase assay (IPA), adapted for detection of serum IgM antibodies to cytomegalovirus (CMV) is described. The antigen consisted of CMV infected human embryonic fibroblasts or isolated nuclei. The sera were absorbed with aggregated gamma-globulins prior to testing. Rabbit anti-human IgM peroxidase conjugate was used to detect IgM bound to viral antigen. In parallel the enzyme linked immunosorbent assay (ELISA) technique was used to determine IgG and IgM antibodies to CMV, respectively. All patients with acute CMV infections who were tested had CMV-specific IgM antibodies by IPA, both whole cell and nuclei antigen. The maximal IgM titers were higher by ELISA than by IPA but in 3 of the CMV patients IgM was detected earlier by IPA (with both types of antigens) than by ELISA. In 3 of 5 transplant patients with recurrent CMV infection IgM was demonstrated by immunoperoxidase techniques, while by ELISA IgM was demonstrated in only 2 of them. No cross reactivity with other herpes viruses was observed. The described IPA is simple, rapid and has the potential for widespread use in routine laboratories.

Adult↗